Contacts of the helix formed by residues 1038 - 1051 (chain D) in PDB entry 4DAJ
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER1038 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1034D THR* 4.2 1.7 - - - +
1036D SER* 3.3 10.0 - - - +
1037D PRO* 1.3 84.0 - - - +
1039D LEU* 1.3 64.7 + - - +
1040D ASN* 3.6 22.7 + - - +
1041D ALA* 3.5 23.5 + - - +
1042D ALA 3.8 2.3 + - - -
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Residues in contact with LEU1039 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1017D ILE* 4.0 19.1 - - + -
1025D TYR* 3.3 42.2 - - + +
1037D PRO 3.1 5.4 + - - -
1038D SER* 1.3 69.1 + - - +
1040D ASN* 1.3 61.2 + - - +
1041D ALA 3.0 2.2 - - - -
1042D ALA* 2.7 29.6 + - + +
1043D LYS* 2.9 35.2 + - + +
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Residues in contact with ASN1040 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1038D SER* 3.3 11.2 + - - +
1039D LEU* 1.3 78.9 - - - +
1041D ALA* 1.3 57.3 + - - +
1043D LYS* 3.9 7.6 - - - +
1044D SER* 2.9 36.1 + - - +
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Residues in contact with ALA1041 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1034D THR* 4.3 5.6 - - + +
1036D SER* 3.6 18.4 - - - +
1038D SER* 3.5 19.4 + - - +
1039D LEU 3.0 0.2 - - - -
1040D ASN* 1.3 76.2 - - - +
1042D ALA* 1.3 67.8 + - - +
1044D SER* 3.0 6.7 + - - -
1045D GLU* 2.9 25.7 + - - +
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Residues in contact with ALA1042 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1017D ILE* 4.5 2.0 - - + -
1025D TYR* 3.7 25.6 - - + -
1033D LEU* 4.0 18.6 - - + +
1034D THR* 3.6 26.5 - - + +
1039D LEU* 2.7 21.6 + - + +
1041D ALA* 1.3 75.5 - - - +
1043D LYS* 1.3 58.0 + - - +
1045D GLU* 3.4 3.8 + - - +
1046D LEU* 2.9 28.8 + - - +
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Residues in contact with LYS1043 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1017D ILE* 3.5 26.7 - - + -
1039D LEU* 2.9 39.7 + - + +
1040D ASN* 4.0 8.3 - - - +
1042D ALA* 1.3 72.9 - - - +
1044D SER* 1.3 56.1 + - - +
1046D LEU* 3.1 9.4 - - + +
1047D ASP* 2.6 44.8 + - - +
1054D THR* 5.1 1.3 - - - +
1055D ASN* 3.3 35.2 + - - +
1056D GLY* 4.0 12.9 - - - +
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Residues in contact with SER1044 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1040D ASN* 2.9 22.2 + - - +
1041D ALA* 3.6 5.2 - - - -
1043D LYS* 1.3 76.1 - - - +
1045D GLU* 1.3 64.1 + - - +
1047D ASP* 3.2 8.1 + - - +
1048D LYS* 2.9 25.4 + - - +
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Residues in contact with GLU1045 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1031D HIS* 5.8 3.8 - - - +
1032D LEU 5.9 0.2 - - - +
1033D LEU* 4.2 25.1 - - + +
1034D THR* 5.7 1.3 - - - -
1041D ALA 2.9 15.7 + - - +
1042D ALA* 3.7 4.9 - - - +
1044D SER* 1.3 75.2 - - - +
1046D LEU* 1.3 65.3 - - - +
1048D LYS* 3.4 31.1 + - - +
1049D ALA* 2.9 22.3 + - + +
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Residues in contact with LEU1046 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1017D ILE* 3.9 28.7 - - + -
1027D ILE* 3.8 30.7 - - + -
1031D HIS* 5.7 0.7 - - + -
1033D LEU* 3.9 13.2 - - + +
1042D ALA 2.9 14.6 + - - +
1043D LYS* 3.1 10.1 - - - +
1045D GLU* 1.3 75.3 - - - +
1047D ASP* 1.3 54.9 + - - +
1049D ALA* 2.6 30.1 + - + +
1050D ILE* 2.9 28.3 + - + -
1054D THR* 3.0 33.7 - - + +
1056D GLY* 4.3 5.4 - - - +
1058D ILE* 4.6 4.9 - - + -
1066D LEU* 5.1 5.2 - - + -
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Residues in contact with ASP1047 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1043D LYS* 2.6 32.3 + - - +
1044D SER* 3.7 7.0 - - - +
1046D LEU* 1.3 70.6 - - - +
1048D LYS* 1.3 55.9 + - - +
1051D GLY* 2.4 37.4 + - - -
1052D ARG 3.3 14.8 + - - +
1053D ASN* 4.6 6.3 - - - +
1054D THR* 2.6 46.5 + - - -
1055D ASN 4.3 0.7 + - - -
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Residues in contact with LYS1048 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1044D SER 2.9 13.3 + - - +
1045D GLU* 3.4 35.7 - - - +
1047D ASP* 1.3 77.1 - - - +
1049D ALA* 1.3 60.6 - - - +
1051D GLY* 3.9 5.8 + - - -
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Residues in contact with ALA1049 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1031D HIS* 4.8 18.4 - - + +
1045D GLU* 2.9 13.0 + - + +
1046D LEU* 2.6 21.6 + - + +
1048D LYS* 1.3 73.6 - - - +
1050D ILE* 1.3 62.6 + - + +
1051D GLY* 4.7 0.2 - - - -
1066D LEU* 4.6 19.5 - - + +
1069D GLN* 5.2 6.9 + - - +
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Residues in contact with ILE1050 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1046D LEU* 2.9 19.4 + - + +
1047D ASP 4.2 0.2 - - - +
1049D ALA* 1.3 75.2 - - - +
1051D GLY* 1.3 61.9 + - - +
1052D ARG* 3.8 27.5 - - + +
1054D THR* 4.0 26.5 - - + -
1058D ILE* 4.6 5.2 - - + -
1062D GLU* 3.6 40.4 - - + +
1066D LEU* 3.6 33.4 - - + -
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Residues in contact with GLY1051 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1047D ASP 2.4 21.6 + - - -
1048D LYS* 4.3 6.1 - - - -
1049D ALA 3.3 1.8 - - - -
1050D ILE* 1.3 76.4 - - - +
1052D ARG* 1.3 59.0 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il